Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,907,691	T→A	10.4%	Q335L (CAG→CTG)	hasE ←	secretion metalloprotease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,907,691	0	T	A	10.4%	126.0 / 6.2	48	Q335L (CAG→CTG)	hasE	secretion metalloprotease
Reads supporting (aligned to +/- strand):  ref base T (21/22);  new base A (2/3);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.56e-01

GGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGC  >  NC_002947/2907561‑2907833                                                                                                                                    |                                                                                                                                               ggcggAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGc                                                                                                                               <  4:329218/148‑1 (MQ=255) ggcggAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCg                                                                                                                              >  8:38171/1‑149 (MQ=255) ggcggAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCAGCCGCTGCAGGTCGatgc                                                                                                                              <  3:76528/149‑4 (MQ=255) ggcggAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCAGCCGCTGCAGGTCGatg                                                                                                                               <  2:121266/148‑3 (MQ=255)              tttACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGGCGAGCGGTACCACTTCCAt                                                                                                                 >  6:280433/1‑149 (MQ=255)                  cccGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGAt                                                                                                              <  7:38171/148‑1 (MQ=255)                  cccGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATc                                                                                                             <  2:229002/149‑1 (MQ=255)                  cccGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATc                                                                                                             >  1:229002/1‑149 (MQ=255)                                  ctgCGTCTGCGCATGGTTGAAGGCCTGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTgg                                                                                              <  7:159828/146‑1 (MQ=255)                                   ggcggcTGCGCTTGGTTGAAGGCCGGGAAGGCGATGTCCACTGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGAGCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGgat                                                                                            <  4:54461/149‑1 (MQ=255)                                   ggCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAATGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGga                                                                                             <  4:291385/148‑1 (MQ=255)                                    gCGTCTGCGCATGGTTGACGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGgatg                                                                                           <  2:282948/149‑1 (MQ=255)                                      gTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGgatgat                                                                                         <  5:37618/149‑1 (MQ=255)                                       tCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGatgatg                                                                                        <  8:261455/149‑1 (MQ=255)                                                ggTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGGATCGCCTGCACCGGGATCAACGCATCGCCCTGCAGCGGCTGGTCTAGCGGTACCACTTCAATGATCTTGGCCCCGGGCTGGATGATGCCGCCGAc                                                                                >  1:90601/1‑149 (MQ=255)                                                  ttGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCa                                                                                                                  >  6:215645/1‑112 (MQ=255)                                                  ttGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCa                                                                                                                  <  5:215645/112‑1 (MQ=255)                                                     aaGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTgg                                                                           <  4:33441/148‑1 (MQ=255)                                                       ggCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGa                                                                        >  7:7869/1‑149 (MQ=255)                                                        gCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGAt                                                                       >  3:295276/1‑149 (MQ=255)                                                           gggAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCt                                                                    <  7:128567/149‑1 (MQ=255)                                                                   gATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGAACTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCt                                                            >  6:36062/1‑149 (MQ=255)                                                                   gATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCAGCACCGGGATCATCGCATCGACCTGCAGCCGCTGGTCGACCCGTACCACTTCCATGAACTTGGCCCCGGGCTCGATGAAGCCCCCGACCGAGGCGATGCTCAGGCACt                                                            >  6:30942/1‑149 (MQ=255)                                                                    aTGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTg                                                           >  5:168093/1‑149 (MQ=255)                                                                     tGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTgg                                                          <  8:7869/149‑1 (MQ=255)                                                                        ccACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTCGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGAc                                                        >  3:121323/1‑148 (MQ=255)                                                                          aCGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCAt                                                     >  8:159943/1‑149 (MQ=255)                                                                                    cTGGGACCATCTTGTC‑GATCGCCTGTACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCa                                                                  >  1:200439/1‑126 (MQ=255)                                                                                    cTGGGACCATCTTGTC‑GATCGCCTGTACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCa                                                                  <  2:200439/126‑1 (MQ=255)                                                                                     tGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCg                                          >  3:138317/1‑149 (MQ=255)                                                                                       ggACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTg                                                           <  7:64288/130‑1 (MQ=255)                                                                                       ggACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATAGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTg                                                           >  8:64288/1‑130 (MQ=255)                                                                                           cATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGc                                    <  5:111799/149‑1 (MQ=255)                                                                                             tCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCg                                   >  1:238338/1‑148 (MQ=255)                                                                                                 gTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGAt                                <  2:238338/147‑1 (MQ=255)                                                                                                      aTCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCgt                          >  4:122879/1‑149 (MQ=255)                                                                                                      aTCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCgt                          <  2:69763/149‑1 (MQ=255)                                                                                                               aCCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCAc                 <  6:168093/149‑1 (MQ=255)                                                                                                                 cGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTgg                      >  2:22094/1‑142 (MQ=255)                                                                                                                 cGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTgg                      <  1:22094/142‑1 (MQ=255)                                                                                                                 cGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATATTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACtt               >  1:260428/1‑149 (MQ=255)                                                                                                                   ggATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCa             <  2:93790/149‑1 (MQ=255)                                                                                                                          cgcatcgACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTc        >  8:186207/1‑147 (MQ=255)                                                                                                                              tcgACCAGCCGCTGCAGGTCGAGCGGTACCACTTTCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTgg                      <  7:19008/129‑1 (MQ=255)                                                                                                                              tcgACCAGCCGCTGCAGGTCGAGCGGTACCACTTTCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTgg                      >  8:19008/1‑129 (MQ=255)                                                                                                                              tcgACCAGCCGCTGCAGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTgc  >  4:214376/1‑149 (MQ=255)                                                                                                                                 aCCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGAt                                >  7:64133/1‑116 (MQ=255)                                                                                                                                 aCCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGAt                                <  8:64133/116‑1 (MQ=255)                                                                                                                                    |                                                                                                                                               GGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTC‑GATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGC  >  NC_002947/2907561‑2907833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑